Collection are one potential answer for how users can specify the set
of stuff that belongs in the directory. For explicitly dealing with
applications that consume directories - I think it is best to just
create the directory and link in files (if possible) before the tool
runs.

<command>mkdir input_dir;
#for $i, $input_file in enumerate($input_files)# ln -s "$input_file"
"input_dir/$i"; #end for
my_application input_dir
</command>
<inputs>
<param name="input_files" type="data" format="bam" multiple="true" />
...
You can also do this sort of thing in a wrapper. If needed you can
build more interesting command-lines this way that add extensions, use
names, etc.... peptideshaker is an example of a fairly complex tool
that uses an idiom like this and doesn't resort to a helper wrapper
(https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=13a5bad5c984db6f#).
I am currently working on support for tools that actually produce
collections of files this way - I think I will probably land up adding
some high-level utilities for doing stuff like this for those
scenarios. But if you tool just produces a couple files and consume a
directory - no need to necessarily resort to collections (as the tool
author - your users will probably want to if they want to use these
tools in workflows).
-John
On Tue, Sep 2, 2014 at 9:51 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> You might be able to do this by accepting a collection of
> SAM/BAM files as input instead. This is a quite new feature
> in Galaxy, see:
>
> https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution
>
> Peter
>
> On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet
> <philippe.m...@gmail.com> wrote:
>> Hi,
>>
>> I am trying to write a wrapper for a tool that take a directory containing
>> SAM/BAM files as an input. I am not sure how to do that, is there another
>> tool that implements this and that I can have a look at ? Any suggestions
>> would be greatly appreciated.
>>
>> Regards,
>> Philip
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/